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Bone_Marrow: WGCNA Modules and Pathway enrichments

Weighted gene coexpression analysis (WGCNA) of the Bone_Marrow RNA-seq resulted in identification of modules comprising of protein coding genes and lncRNAs with correlated expression patterns. The genes in the coexpression modules were subjected to pathway enrichment to identify pathways in which the genes in the modules significantly enrich. Shown below is a graphical summary comprising of the modules and the pathways terms to which the genes in the respective module associate with. Viewers can shortlist the modules of interest based on the biological process of interest.

 

Graphical Summary of WGCNA modules

 

Significant Modules/Pathways

Genes in the coexpression modules identified by WGCNA analysis were further analyzed for pathway enrichment. All the pathways in which the genes from the coexpression modules significantly (q value < 0.05) enrich for are presented below. Viewers can browse the table or search for key pathway terms in the "search" window.
Full pathway enrichment results and the adjacency matrix of the modules of interest can be downloaded below:
Download: [ Modules Full list (CSV), Adjacency Matrices (tar.gz) ] or 
Adjacency Matrix per Module:
    M1 module
    M2 module
    M3 module
    M4 module
    M5 module
    M6 module
    M7 module
    M8 module
    M9 module
    M10 module
    M11 module
    M12 module
    M13 module
    M14 module
    M15 module
    M16 module
    M17 module
    M18 module
    M19 module
    M20 module
    M21 module
    M22 module
    M23 module
    M24 module

 

 

Notable Pathways:

To facilitate network analysis of the Bone_Marrow RNA seq data, 25 notable pathways from the pathway enrichment data was selected. For each pathway, network image and json file was generated that comprises of the gene (in the indicated pathway) along with correlated lncRNAs. Viewers can look at the PNG file to view the network of download and open the cyjs file in Cytoscape for further exploration. (Green circular nodes: protein-coding genes, Orange triangle: lncRNAs)
 Module   ID  Gene Ratio  qvalue  Gene Count  Total Genes in module   lncrnas in module   Plot  Cytoscape JSON file
 M1  GO CELL DIVISION   34/630   0.023568656  34  770  222  cyjs file 
 M19  GO CELL DIVISION   45/849   0.003835459  45  1006  169  cyjs file 
 M19  GO MITOTIC NUCLEAR DIVISION   43/849   0.000100712  43  1006  169  cyjs file 
 M19  GO REGULATION OF MITOTIC CELL CYCLE   41/849   0.022283268  41  1006  169  cyjs file 
 M19  GO CELL CYCLE PHASE TRANSITION   38/849   4.59E-06  38  1006  169  cyjs file 
 M19  GO CHROMOSOMAL REGION   38/849   0.000663939  38  1006  169  cyjs file 
 M23  GO DNA REPAIR   78/1898   0.030288088  78  2293  1153  cyjs file 
 M23  GO RESPONSE TO RADIATION   70/1898   0.02395564  70  2293  1153  cyjs file 
 M23  GO GOLGI VESICLE TRANSPORT   62/1898   0.00383242  62  2293  1153  cyjs file 
 M23  GO MICROTUBULE CYTOSKELETON ORGANIZATION   61/1898   0.02395564  61  2293  1153  cyjs file 
 M23  GO UBIQUITIN LIGASE COMPLEX   55/1898   0.002063292  55  2293  1153  cyjs file 
 M23  GO CHROMOSOME SEGREGATION   49/1898   0.035038223  49  2293  1153  cyjs file 
 M23  GO CELLULAR RESPONSE TO PEPTIDE   49/1898   0.03730465  49  2293  1153  cyjs file 
 M23  GO REGULATION OF NUCLEOCYTOPLASMIC TRANSPORT   44/1898   0.018331609  44  2293  1153  cyjs file 
 M23  GO ER TO GOLGI VESICLE MEDIATED TRANSPORT   34/1898   0.030288088  34  2293  1153  cyjs file 
 M23  GO RESPONSE TO UV   32/1898   0.003035592  32  2293  1153  cyjs file 
 M23  GO CELLULAR RESPONSE TO RADIATION   32/1898   0.01089451  32  2293  1153  cyjs file 
 M3  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO ORGANELLE   67/1036   2.24E-14  67  1237  799  cyjs file 
 M3  GO PROTEIN LOCALIZATION TO MEMBRANE   57/1036   1.26E-08  57  1237  799  cyjs file 
 M3  GO MITOCHONDRIAL MATRIX   56/1036   9.09E-07  56  1237  799  cyjs file 
 M3  GO ESTABLISHMENT OF PROTEIN LOCALIZATION TO MEMBRANE   51/1036   1.49E-11  51  1237  799  cyjs file 
 M3  GO CYTOKINE MEDIATED SIGNALING PATHWAY   45/1036   0.021230592  45  1237  799  cyjs file 
 M3  GO CELLULAR RESPIRATION   43/1036   1.49E-16  43  1237  799  cyjs file 
 M3  GO REGULATION OF CELL CYCLE PHASE TRANSITION   39/1036   0.001267653  39  1237  799  cyjs file